Align Methylmalonyl-CoA epimerase; DL-methylmalonyl-CoA racemase; EC 5.1.99.1 (characterized)
to candidate WP_036833956.1 N784_RS07955 methylmalonyl-CoA epimerase
Query= SwissProt::O58010 (136 letters) >NCBI__GCF_000775615.1:WP_036833956.1 Length = 276 Score = 140 bits (354), Expect = 1e-38 Identities = 63/129 (48%), Positives = 99/129 (76%), Gaps = 1/129 (0%) Query: 6 KRIDHVGIAVKNLEEAIKIW-EGLGFKVEEIEEVPDQKVKVAVIKVGENRIELLEATTED 64 +++ H+GIAV ++E+A+ + LG ++ +EEV ++VKVA +++GE +IELLE T ++ Sbjct: 142 EKLAHIGIAVNSIEQALPFYTNALGLRLTGVEEVASEQVKVAFVEIGETQIELLEPTDDN 201 Query: 65 SPIAKFIEKRGEGIHHLAIRVENIESKLEELKQKGYKLIDEKPRVGAGGAKIAFIHPKSV 124 SPIAKF+EKRGEGIHH+A+ V +IE +L K+KG LI + P++GA +++AF+HPK+ Sbjct: 202 SPIAKFMEKRGEGIHHIAVEVTDIEERLRHYKEKGISLIHDTPKLGAHQSQVAFLHPKAT 261 Query: 125 TGVLLELCE 133 GVL+ELC+ Sbjct: 262 NGVLMELCQ 270 Lambda K H 0.317 0.138 0.389 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 139 Number of extensions: 5 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 136 Length of database: 276 Length adjustment: 20 Effective length of query: 116 Effective length of database: 256 Effective search space: 29696 Effective search space used: 29696 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 44 (21.6 bits)
Align candidate WP_036833956.1 N784_RS07955 (methylmalonyl-CoA epimerase)
to HMM TIGR03081 (mce: methylmalonyl-CoA epimerase (EC 5.1.99.1))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR03081.hmm # target sequence database: /tmp/gapView.1555738.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03081 [M=129] Accession: TIGR03081 Description: metmalonyl_epim: methylmalonyl-CoA epimerase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-51 160.6 1.4 2e-51 160.0 0.6 1.7 2 NCBI__GCF_000775615.1:WP_036833956.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000775615.1:WP_036833956.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -2.9 0.0 0.49 0.49 31 54 .. 27 50 .. 24 63 .. 0.63 2 ! 160.0 0.6 2e-51 2e-51 1 129 [] 143 270 .. 143 270 .. 0.99 Alignments for each domain: == domain 1 score: -2.9 bits; conditional E-value: 0.49 TIGR03081 31 eelpeqgvkvvflelgetklelle 54 ++l ++g++v++ l ++ ++++ NCBI__GCF_000775615.1:WP_036833956.1 27 QALRDHGMEVIYTGLRQSPQQIVQ 50 556777777777777666555554 PP == domain 2 score: 160.0 bits; conditional E-value: 2e-51 TIGR03081 1 kldhvaiavkdleeaaklyrdvlGakvseeeelpeqgvkvvflelgetklellepleedspiakflekkkgeG 73 kl h++iav+++e+a +y+++lG++++ ee++ ++vkv+f+e+get++ellep++++spiakf+ek+ geG NCBI__GCF_000775615.1:WP_036833956.1 143 KLAHIGIAVNSIEQALPFYTNALGLRLTGVEEVASEQVKVAFVEIGETQIELLEPTDDNSPIAKFMEKR-GEG 214 689******************************************************************.*** PP TIGR03081 74 lhhialevddieaaletlkekgvrlldeepriGahGkkvaFlhPkdtgGvLielee 129 +hhia+ev+die+ l++ kekg+ l++++p++Gah +vaFlhPk t+GvL+el++ NCBI__GCF_000775615.1:WP_036833956.1 215 IHHIAVEVTDIEERLRHYKEKGISLIHDTPKLGAHQSQVAFLHPKATNGVLMELCQ 270 ******************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (129 nodes) Target sequences: 1 (276 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 11.59 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory